Our works centers on the genetic basis for microbial influence of animal traits. Students in the lab focus on one of three technical areas:
1) Drosophila behavior, physiology, and genetics. The fruit fly Drosophila melanogaster is a superb model organism for investigating animal responses to associated microbes, including in mammals. It has a culturable, low diversity microbiota, and many of its behavioral and physiological traits are strongly influenced by microbiota. We dissect the contributions of specific microbes to these traits by first eliminating colonizing microbes from Drosophila embryos, and then inoculating embryos with target microbial species of interest. We also draw on vast community resources in the Drosophila field to understand how host genotype dictates and responds to the presence of particular microbial taxa.
2) Microbial genetics. We use genetic approaches to dissect the mechanistic basis for bacterial influence of animal traits. Most bacteria that associate with Drosophila are readily cultured and are amenable to genetic interrogation. These approaches are increasingly supported by genomic tools, including next-generation sequencing-based approaches. We are also interested in developing genetic approaches in bacteria that are recalcitrant to standard laboratory culture and mutagenesis techniques.
3) Bioinformatics. To support both of the research areas above we use comparative and statistical genomic approaches that require use or modification of existing bioinformatics tools, or development of new approaches. We are particularly focused on our recent development of a metagenome-wide association pipeline as a surrogate for a functional genetic screen. This approach successfully predicted bacterial genes that affect host traits from phenotypic data collected from a relatively small number (41) of mono associated hosts. We are currently developing this and other tools for public dissemination.